data_3KOD
#
_model_server_result.job_id            oHWLO3-krM1KQPhZEAL9fQ 
_model_server_result.datetime_utc      '2024-10-12 04:22:49' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          3kod 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":165}' 
#
_entry.id    3KOD 
#
_exptl.entry_id    3KOD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              105.093 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            D-SERINE 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         106.86 
_cell.angle_beta          101.86 
_cell.angle_gamma         94.45 
_cell.entry_id            3KOD 
_cell.length_a            52.281 
_cell.length_b            55.147 
_cell.length_c            92.535 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KOD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G 1 1 
C,D,H,I,J 2 1 
E,F 3 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
#
_chem_comp.formula           'C3 H7 N O3' 
_chem_comp.formula_weight    105.093 
_chem_comp.id                DSN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              D-SERINE 
_chem_comp.type              'd-peptide linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
N CA DSN sing 83 n n 
N H DSN sing 84 n n 
N H2 DSN sing 85 n n 
CA C DSN sing 86 n n 
CA CB DSN sing 87 n n 
CA HA DSN sing 88 n n 
C O DSN doub 89 n n 
C OXT DSN sing 90 n n 
OXT HXT DSN sing 91 n n 
CB OG DSN sing 92 n n 
CB HB2 DSN sing 93 n n 
CB HB3 DSN sing 94 n n 
OG HG DSN sing 95 n n 
#
_atom_sites.entry_id                     3KOD 
_atom_sites.fract_transf_matrix[1][1]    0.019127 
_atom_sites.fract_transf_matrix[1][2]    0.001488 
_atom_sites.fract_transf_matrix[1][3]    0.004722 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018188 
_atom_sites.fract_transf_matrix[2][3]    0.006008 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011629 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
G 2 DSN B 1 165 1 DSN DSN . 
H 2 DSN C 1 165 1 DSN DSN . 
I 2 DSN D 1 165 1 DSN DSN . 
J 2 DSN D 1 166 1 DSN DSN . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N DSN . . . H 2 -23.046 -12.413 30.346 1 105.43 ? N DSN 165 C 1 
HETATM 2 C CA DSN . . . H 2 -23.316 -11.927 28.954 1 105.44 ? CA DSN 165 C 1 
HETATM 3 C C DSN . . . H 2 -23.702 -10.463 28.904 1 105.41 ? C DSN 165 C 1 
HETATM 4 O O DSN . . . H 2 -23.765 -9.873 27.822 1 105.31 ? O DSN 165 C 1 
HETATM 5 O OXT DSN . . . H 2 -23.988 -9.828 29.931 1 105.2 ? OXT DSN 165 C 1 
HETATM 6 C CB DSN . . . H 2 -22.155 -12.329 28.022 1 105.34 ? CB DSN 165 C 1 
HETATM 7 O OG DSN . . . H 2 -21.268 -11.237 27.724 1 105.32 ? OG DSN 165 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           7 
#